I am trying to apply no patch on the N-terminal residue,as I am missing the first 8 residues. Howeverm I get the error message that I am missing HN coordinates so that in the end they look like 9999.000 9999.000 9999.000.
When you apply NTER to the same case, it works like a charm.
I suppose I am just missing some keyword or I am not seeing the error. All in all, I would appreciate your help.
How do you plan to deal with the connectivity for the N atom? The AA residues are defined in the topology file with implied bonds to previous and next residues, so something must be done at the ends of the polymer chains to avoid problems. For the N-terminal residue, the ACE patch is commonly used for truncated sequences; it adds an acetyl group to create an amide, and satisfy connectivity w/o adding a + charge.
The default terminal patches for nucleic acids are NONE, which is not OK. You have to specify whether you want a charged (-1) phosphate (5PHO, 3PHO) or a non-charged hydroxyl (5TER, 3TER) at either end; both exist in nature, so the user has to make the decision, and that is also why there is no default patch. One often wants to avoid having many charges so 5TER and 3TER are commonly used. In your case the phoshpate might be more appropriate. It is also quite easy to model a couple of missing nucleotides at the end.
Lennart Nilsson Karolinska Institutet Stockholm, Sweden